def test_remove_empty_fields(self):
assert dict(some_str="something") == Instruction._remove_empty_fields(
{"some_str": "something", "empty": None})
assert dict(some_str="something", dict_1=dict(some_int=1)) == \
Instruction._remove_empty_fields(
{"some_str": "something", "empty": None,
"dict_1": {"some_int": 1, "empty": None}})
assert [dict(some_bool=True)] == \
Instruction._remove_empty_fields(
[dict(some_bool=True, empty=None)])
assert [dict(some_bool=True)] == \
Instruction._remove_empty_fields(
[dict(some_bool=True, empty={})])
assert [dict(some_bool=True)] == \
Instruction._remove_empty_fields(
[dict(some_bool=True, empty=[])])
assert Instruction(op="some instruction",
data={
"not_empty": {"foo": "bar"},
"empty": {
"foo": None, "bar": None
}
}).data == {"not_empty": {"foo": "bar"}}
assert Instruction(op="some instruction",
data={
"not_empty": ["foo", "bar"],
"empty": [None, None]
}).data == {"not_empty": ["foo", "bar"]}
def test_get_wells(self):
p = Protocol()
cont1 = p.ref("cont1", None, "6-flat", discard=True)
cont2 = p.ref("cont2", None, "6-flat", discard=True)
example_data = {
"list": [cont1.well(0), cont1.well(1)],
"well": cont2,
"dict": {"key1": 1, "key2": "bar", "dict_well": cont1.well(2)},
"bar": [
{"key4": "value", "key5": {"well": cont1.well(3)}},
{"key4": "value", "key5": {"well_group": WellGroup([cont1.well(4)])}},
],
"duplicate": cont1.well(0),
"nest": [{"list": [{"more_nested": [{"wells": [cont1.well(5)]}]}]}],
}
inst = Instruction(op="test", data=example_data)
wells = set(cont1.all_wells().wells + cont2.all_wells().wells)
assert set(inst.get_wells(example_data)) == wells
def test_remove_empty_fields(self):
assert dict(some_str="something") == Instruction._remove_empty_fields({
"some_str":
"something",
"empty":
None
})
assert dict(
some_str="something",
dict_1=dict(some_int=1)) == Instruction._remove_empty_fields({
"some_str":
"something",
"empty":
None,
"dict_1": {
"some_int": 1,
"empty": None
},
})
assert [dict(some_bool=True)] == Instruction._remove_empty_fields(
[dict(some_bool=True, empty=None)])
assert [dict(some_bool=True)] == Instruction._remove_empty_fields(
[dict(some_bool=True, empty={})])
assert [dict(some_bool=True)] == Instruction._remove_empty_fields(
[dict(some_bool=True, empty=[])])
assert Instruction(
op="some instruction",
data={
"not_empty": {
"foo": "bar"
},
"empty": {
"foo": None,
"bar": None
}
},
).data == {
"not_empty": {
"foo": "bar"
}
}
assert Instruction(
op="some instruction",
data={
"not_empty": ["foo", "bar"],
"empty": [None, None]
},
).data == {
"not_empty": ["foo", "bar"]
}
def test_instruction(self):
example_data = {
"dict_1": {
"dict_1a": {
"empty": None,
"some_int": 12,
"list_1": [{"empty": None, "some_str": "something"}, {}],
}
},
"empty": None,
"dict_2": {"empty": None, "empty_list": [], "some_bool": False},
}
return Instruction(op="test_instruction", data=example_data)
def test_info_wells_checker(self):
p = Protocol()
cont1 = p.ref("cont1", None, "6-flat", discard=True)
compd = Compound("Daylight Canonical SMILES", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
example_data = {"objects": [cont1.well(0), cont1.well(1)], "some_int": 1}
instr = Instruction(
op="test_instruction",
data=example_data,
informatics=[AttachCompounds(cont1.well(0), [compd])],
)
avail_wells = instr.get_wells(instr.data)
with pytest.raises(ValueError):
instr.informatics[0].wells = None
instr._check_info_wells(instr.informatics[0], avail_wells)
with pytest.raises(TypeError):
instr.informatics[0].wells = "cont1/0"
instr._check_info_wells(instr.informatics[0], avail_wells)
with pytest.raises(ValueError):
instr.informatics[0].wells = cont1.well(10)
instr._check_info_wells(instr.informatics[0], avail_wells)
def test_informatics():
p = Protocol()
cont1 = p.ref("cont1", None, "6-flat", discard=True)
compd = Compound("Daylight Canonical SMILES", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
example_data = {
"wells": [cont1.well(0), cont1.well(1)],
"some_int": 1,
}
example_informatics = [AttachCompounds(cont1.well(0), [compd])]
instr = Instruction(
op="test_instruction", data=example_data, informatics=example_informatics
)
assert isinstance(instr.informatics[0], AttachCompounds)
assert instr.informatics[0].compounds[0].value == "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
instr_multi = Instruction(
op="test_instruction",
data=example_data,
informatics=[
AttachCompounds(cont1.well(0), [compd]),
AttachCompounds(cont1.well(1), [compd]),
],
)
assert len(instr_multi.informatics) == 2
def test_laser_builder(self):
assert self.laser_reference == FlowCytometry.builders.laser(
**self.laser_reference)
assert (self.valid_gating_mode_laser_reference ==
Instruction._remove_empty_fields(
FlowCytometry.builders.laser(
**self.valid_gating_mode_laser_reference)))
# Cannot specify excitation if gating mode specified
with pytest.raises(ValueError):
FlowCytometry.builders.laser(
**{
**self.valid_gating_mode_laser_reference,
**{
"excitation": "400:nanometer"
},
})